1000 x 1000 human genomes in five years

Huntington’s disease project to sequence an unprecedented 100 human genomes in first six months

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MOUNTAIN VIEW, Calif.— The Institute for Systems Biology (ISB) has engaged Complete Genomics Inc. to sequence 100 genomes, the majority of which will be used to investigate Huntington's Disease (HD), with samples from affected individuals, family members and matched controls to study modifiers of disease presentation and progression. This will be the largest complete human genome disease association study conducted to date, and will be the first 100-genome study produced by Complete Genomics in its newly expanded sequencing facility. And as Al Jolson once famously said to moviegoers, "You ain't seen nothin' yet."

The Seattle-based nonprofit research institute was established in 2000 with the goal of unraveling the mysteries of complex biological systems to predict and prevent diseases such as cancer diabetes and AIDS. For the HD study, ISB will supply the purified DNA samples, and Complete Genomics will sequence and identify variations for each genome. ISB will then do the genetic analysis at the sequence level.

"We were pleased with the quality of the raw sequencing data and variations reports that Complete Genomics generated for our four-genome pilot project earlier this year. Its sequencing technology has the requisite accuracy, consistency and low price point to enable us to begin conducting this large-scale genomic study in this important patient population," says ISB President Dr. Leroy Hood.

The goal at Complete Genomics, says Dr. Clifford Reid, company chairman, president and CEO, is nothing less than to sequence 1 million genomes over the next five years. Long-term, he says, genome testing will be as common as blood tests.

"We're right at the beginning of the process," Reid says. "Our customers will be able to conduct 1,000 studies of 1,000 people to understand the genetic basis of all human disease."

Sequencing 100 genomes in six months for the HD study is a relatively humble, but important, beginning. The comparison of healthy and diseased complete human genome sequences will enable genome-wide association studies with a focus on rare, single-nucleotide polymorphisms (SNPs), and insertions and deletions that are incompletely accessible with current genomewide SNP chip technologies, according to Reid. These will include rare variants in protein coding regions of the genome (the "exome") as well as in regulatory regions.

Currently, Complete Genomics is busy converting offices in its headquarters building into additional sequencing labs. As the ramp-up continues, Reid says the company expects 2010 output to reach 10,000 sequenced genomes and the totals to continue growing from there.

"It is when we start to look at genomics research on this scale that our sequencing technology really comes into its own, and we have the potential to make truly revolutionary discoveries," says Reid.

He notes that first-generation Sanger sequencing technology used capillary electrophoresis and cost $10 million per genome. Second generation short-read technology reduced the cost initially to about $1 million, and more recently, to about $100 thousand. Third-generation Complete Genomics technology reduces the cost per genome to under $10,000 on its way to $5,000 and lower.

The three-and-a-half-year-old company owes its technology to its founder and CSO, Dr. Radoje Drmanac, a leading researcher in the field of DNA sequencing-by-hybridization (SBH). Cliff Reid provides the computer savvy needed to launch genome sequencing as a commercial process. Complete Genomics uses a systems approach, he notes.

"Not only do we engineer our own hardware and biochemistry, but also the computer technology that creates a turnkey process," Drmanac says. "We run so fast that customers couldn't handle all the data so we've written all the data management software for a huge computer cluster and send them research-ready data by FedEx." Standard turnaround time on sequencing projects is 90 days, he notes.

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